Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient.

Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.

Comparison of Automated Spike Detection Software in Detecting Epileptiform Abnormalities on Scalp-EEG of Genetic Generalized Epilepsy Patients.

PURPOSE: Despite availability of commercial EEG software for automated epileptiform detection, validation on real-world EEG datasets is lacking. Performance evaluation of two software packages on a large EEG dataset of patients with genetic generalized epilepsy was performed. METHODS: Three epileptologists labelled IEDs manually of EEGs from three centres. All Interictal epileptiform discharge (IED) markings predicted by two commercial software (Encevis 1.11 and Persyst 14) were reviewed individually to assess for suspicious missed markings and were integrated into the reference standard if overlooked during manual annotation during a second phase. Sensitivity, precision, specificity, and F1-score were used to assess the performance of the software packages against the adjusted reference standard. RESULTS: One hundred and twenty-five routine scalp EEG recordings from different subjects were included (total recording time, 310.7 hours). The total epileptiform discharge reference count was 5,907 (including spikes and fragments). Encevis demonstrated a mean sensitivity for detection of IEDs of 0.46 (SD 0.32), mean precision of 0.37 (SD 0.31), and mean F1-score of 0.43 (SD 0.23). Using the default medium setting, the sensitivity of Persyst was 0.67 (SD 0.31), with a precision of 0.49 (SD 0.33) and F1-score of 0.51 (SD 0.25). Mean specificity representing non-IED window identification and classification was 0.973 (SD 0.08) for Encevis and 0.968 (SD 0.07) for Persyst. CONCLUSIONS: Automated software shows a high degree of specificity for detection of nonepileptiform background. Sensitivity and precision for IED detection is lower, but may be acceptable for initial screening in the clinical and research setting. Clinical caution and continuous expert human oversight are recommended with all EEG recordings before a diagnostic interpretation is provided based on the output of the software.

Genomic epidemiological analysis of mcr-1-harboring Escherichia coli collected from livestock settings in Vietnam.

Livestock has been implicated as a reservoir for antimicrobial resistance (AMR) genes that can spread to humans when antimicrobials are used in animals for food production to treat clinical diseases and prevent and control common disease events. In Vietnam, mcr-1-harboring Escherichia coli (MCRPEC) strains have been isolated from humans, animals (chickens, pigs, and dogs) feces, flies, foods, and the environment (rainwater, well water, and irrigation water) in communities and from clinical specimens in hospitals. The relationship between levels of AMR in livestock and its occurrence in humans is complex and is driven by many factors. We conducted whole genome sequencing of MCRPEC to analyze the molecular epidemiological characteristics, history, and relatedness of 50 isolates obtained in 2019 from different reservoirs in farms and markets in Ha Nam province, Vietnam. 34 sequence types (STs) with 3 new STs were identified in multilocus sequence typing analysis: ST12945 and ST12946 from chicken feces, and ST12947 from flies. The AMR phenotypes of 50 MCRPEC isolates were as follows: ampicillin (100%, 50/50), cefotaxime (10%, 5/50), gentamicin (60%, 30/50), amikacin (8%, 4/50), meropenem (6%, 3/50), ceftazidime (18%, 9/50), colistin (24%, 12/50) and ciprofloxacin (80%, 40/50). All 50 MCRPEC isolates were identified as MDR. 100% (50/50) isolates carried AMR genes, ranging from 5 to 22 genes. The most prevalent plasmid replicon types carrying mcr-1 were IncP-1 (17/37, 45.9%), IncX4 (7/37, 18.9%), and IncHI2/IncHI2A (6/37, 16.2%). These data suggest that the epidemiology of the mcr-1 gene is mostly determined by plasmid spreading instead of clonal dissemination of MCRPE strains. The co-occurrence of several STs such as ST10, ST48, ST155, ST206, ST2705 in various sample types, joined to the higher prevalence of a few types of Inc plasmids, confirms the dissemination of the mcr-1 carrying plasmids in E. coli clones established in livestock. 5 over 8 STs identified in flies (ST206, ST2705, ST155, ST10, and ST48) suggested the fly contribution in the transmission of AMR bacteria in environments. These popular STs also occur in human samples and 100% of the human samples were positive for the mcr-1 gene.

Deep learning for automated epileptiform discharge detection from scalp EEG: A systematic review.

Automated interictal epileptiform discharge (IED) detection has been widely studied, with machine learning methods at the forefront in recent years. As computational resources become more accessible, researchers have applied deep learning (DL) to IED detection with promising results. This systematic review aims to provide an overview of the current DL approaches to automated IED detection from scalp electroencephalography (EEG) and establish recommendations for the clinical research community. We conduct a systematic review according to the PRISMA guidelines. We searched for studies published between 2012 and 2022 implementing DL for automating IED detection from scalp EEG in major medical and engineering databases. We highlight trends and formulate recommendations for the research community by analyzing various aspects: data properties, preprocessing methods, DL architectures, evaluation metrics and results, and reproducibility. The search yielded 66 studies, and 23 met our inclusion criteria. There were two main DL networks, convolutional neural networks in 14 studies and long short-term memory networks in three studies. A hybrid approach combining a hidden Markov model with an autoencoder was employed in one study. Graph convolutional network was seen in one study, which considered a montage as a graph. All DL models involved supervised learning. The median number of layers was 9 (IQR: 5-21). The median number of IEDs was 11 631 (IQR: 2663-16 402). Only six studies acquired data from multiple clinical centers. AUC was the most reported metric (median: 0.94; IQR: 0.94-0.96). The application of DL to IED detection is still limited and lacks standardization in data collection, multi-center testing, and reporting of clinically relevant metrics (i.e. F1, AUCPR, and false-positive/minute). However, the performance is promising, suggesting that DL might be a helpful approach. Further testing on multiple datasets from different clinical centers is required to confirm the generalizability of these methods.

Moving the field forward: detection of epileptiform abnormalities on scalp electroencephalography using deep learning-clinical application perspectives.

The application of deep learning approaches for the detection of interictal epileptiform discharges is a nascent field, with most studies published in the past 5 years. Although many recent models have been published demonstrating promising results, deficiencies in descriptions of data sets, unstandardized methods, variation in performance evaluation and lack of demonstrable generalizability have made it difficult for these algorithms to be compared and progress to clinical validity. A few recent publications have provided a detailed breakdown of data sets and relevant performance metrics to exemplify the potential of deep learning in epileptiform discharge detection. This review provides an overview of the field and equips computer and data scientists with a synopsis of EEG data sets, background and epileptiform variation, model evaluation parameters and an awareness of the performance metrics of high impact and interest to the trained clinical and neuroscientist EEG end user. The gold standard and inter-rater disagreements in defining epileptiform abnormalities remain a challenge in the field, and a hierarchical proposal for epileptiform discharge labelling options is recommended. Standardized descriptions of data sets and reporting metrics are a priority. Source code-sharing and accessibility to public EEG data sets will increase the rigour, quality and progress in the field and allow validation and real-world clinical translation.

Preferences and User Experiences of Wearable Devices in Epilepsy: A Systematic Review and Mixed-Methods Synthesis.

BACKGROUND AND OBJECTIVES: To examine the preferences and user experiences of people with epilepsy and caregivers regarding automated wearable seizure detection devices. METHODS: We performed a mixed-methods systematic review. We searched electronic databases for original peer-reviewed publications between January 1, 2000, and May 26, 2021. Key search terms included "epilepsy," "seizure," "wearable," and "non-invasive." We performed a descriptive and qualitative thematic analysis of the studies included according to the technology acceptance model. Full texts of the discussion sections were further analyzed to identify word frequency and word mapping. RESULTS: Twenty-two observational studies were identified. Collectively, they comprised responses from 3,299 participants including patients with epilepsy, caregivers, and healthcare workers. Sixteen studies examined user preferences, 5 examined user experiences, and 1 examined both experiences and preferences. Important preferences for wearables included improving care, cost, accuracy, and design. Patients desired real-time detection with a latency of ≤15 minutes from seizure occurrence, along with high sensitivity (≥90%) and low false alarm rates. Device-related costs were a major factor for device acceptance, where device costs of <$300 USD and a monthly subscription fee of <$20 USD were preferred. Despite being a major driver of wearable-based technologies, sudden unexpected death in epilepsy was rarely discussed. Among studies evaluating user experiences, there was a greater acceptance toward wristwatches. Thematic coding analysis showed that attitudes toward device use and perceived usefulness were reported consistently. Word mapping identified "specificity," "cost," and "battery" as key single terms and "battery life," "insurance coverage," "prediction/detection quality," and the effect of devices on "daily life" as key bigrams. DISCUSSION: User acceptance of wearable technology for seizure detection was strongly influenced by accuracy, design, comfort, and cost. Our findings emphasize the need for standardized and validated tools to comprehensively examine preferences and user experiences of wearable devices in this population using the themes identified in this study. Greater efforts to incorporate perspectives and user experiences in developing wearables for seizure detection, particularly in community-based settings, are needed. TRIAL REGISTRATION INFORMATION: PROSPERO Registration CRD42020193565.

BH3 mimetic drugs cooperate with Temozolomide, JQ1 and inducers of ferroptosis in killing glioblastoma multiforme cells.

Glioblastoma multiforme (GBM) is the most common and aggressive form of brain cancer, with treatment options often constrained due to inherent resistance of malignant cells to conventional therapy. We investigated the impact of triggering programmed cell death (PCD) by using BH3 mimetic drugs in human GBM cell lines. We demonstrate that co-targeting the pro-survival proteins BCL-XL and MCL-1 was more potent at killing six GBM cell lines compared to conventional therapy with Temozolomide or the bromodomain inhibitor JQ1 in vitro. Enhanced cell killing was observed in U251 and SNB-19 cells in response to dual treatment with TMZ or JQ1 combined with a BCL-XL inhibitor, compared to single agent treatment. This was reflected in abundant cleavage/activation of caspase-3 and cleavage of PARP1, markers of apoptosis. U251 and SNB-19 cells were more readily killed by a combination of BH3 mimetics targeting BCL-XL and MCL-1 as opposed to dual treatment with the BCL-2 inhibitor Venetoclax and a BCL-XL inhibitor. The combined loss of BAX and BAK, the essential executioners of intrinsic apoptosis, rendered U251 and SNB-19 cells refractory to any of the drug combinations tested, demonstrating that apoptosis is responsible for their killing. In an orthotopic mouse model of GBM, we demonstrate that the BCL-XL inhibitor A1331852 can penetrate the brain, with A1331852 detected in both tumour and healthy brain regions. We also investigated the impact of combining small molecule inducers of ferroptosis, erastin and RSL3, with BH3 mimetic drugs. We found that a BCL-XL or an MCL-1 inhibitor potently cooperates with inducers of ferroptosis in killing U251 cells. Overall, these findings demonstrate the potential of dual targeting of distinct PCD signalling pathways in GBM and may guide the utility of BCL-XL inhibitors and inducers of ferroptosis with standard of care treatment for improved therapies for GBM.

Ab Initio Investigation of the Hydrogen Interaction on Two Dimensional Silicon Carbide.

A series of density functional theory calculations were performed to understand the bonding and interaction of hydrogen adsorption on two-dimensional silicon carbide obtained from molecular dynamics simulation. The converged energy results pointed out that the H atom can sufficiently bond to 2D SiC at the top sites (atop Si and C), of which the most stable adsorption site is TSi. The vibrational properties along with the zero-point energy were incorporated into the energy calculations to further understand the phonon effect of the adsorbed H. Most of the 2D SiC structure deformations caused by the H atoms were found at the adsorbent atom along the vertical axis. For the first time, five SiC defect formations, including the quadrilateral-octagon linear defect (8-4), the silicon interstitial defect, the divacancy (4-10-4) defect, the divacancy (8-4-4-8) defect, and the divacancy (4-8-8-4) defect, were investigated and compared with previous 2D defect studies. The linear defect (8-4) has the lowest formation energy and is most likely to be formed for SiC materials. Furthermore, hydrogen atoms adsorb more readily on the defect surface than on the pristine SiC surface.

Taxonomical insights and ecology of sandfly (Diptera, Psychodidae) species in six provinces of Northern Vietnam.

We studied sandfly (Diptera: Psychodidae) populations in six provinces of Vietnam. This work explores the diversity of sandfly species according to the province, as well as environment, and updated information on public health since leishmaniasis cases were reported in two provinces. Sandflies were collected using 428 CDC light traps from May 30 to October 13, 2016 and identified based on the morphology of the cibarium, pharynx and/or male genitalia or female spermathecae. A total of 2585 sandflies belonging to five genera and 13 identified species were collected. The main species were: the Sergentomyia barraudi group (12.53%), Se. sylvatica (9.63%) and Phlebotomus stantoni (3.95%). In all, 294 Sergentomyia specimens classified as Se. sp2 and Se. sp3 and a heterogeneous group, herein called Se. und_sp., showed unknown morphological characteristics requiring further studies. We provide detailed comments about morphological description and taxonomical identification in order to help standardization of sandfly classification in Southeast Asia. We observed differentiation according to the provinces in terms of density and species richness, with Lang Son having the highest density and Ninh Binh having the highest species richness. The majority of specimens were collected in rock caves and outdoors, suggesting mainly cavernicolous and exophilic characters of sandfly species in Northern Vietnam. However, specimens were also collected in intra- and peri-domiciliary sites. It is worth noting that Ph. stantoni was the main species found in dog sheds and indoors, and in particular in a leishmaniasis patient's house.

TITLE: Aperçu taxonomique et écologie des espèces de phlébotomes (Diptera, Psychodidae) dans six provinces du nord du Vietnam. ABSTRACT: Nous avons étudié les populations de phlébotomes (Diptera : Psychodidae) dans six provinces du Vietnam. Ce travail explore la diversité des espèces de phlébotomes selon les provinces, les environnements et les informations mises à jour sur la santé publique depuis que des cas de leishmanioses ont été signalés dans deux provinces. Des phlébotomes ont été collectés à l'aide de 428 pièges lumineux CDC du 30 mai au 13 octobre 2016 et identifiés sur la base de la morphologie du cibarium, du pharynx et/ou des organes génitaux des mâles ou des spermathèques des femelles. Au total, 2585 phlébotomes, appartenant à cinq genres et 13 espèces identifiées, ont été collectés. Les principales espèces étaient : le groupe Sergentomyia barraudi (12,53 %), Se. sylvatica (9,63 %) et Phlebotomus stantoni (3,95 %). 294 spécimens de Sergentomyia classés comme Se. sp2 et Se. sp3 et un groupe hétérogène ici appelé Se. und_sp. ont montré des caractéristiques morphologiques inconnues nécessitant des études complémentaires. Nous fournissons des commentaires détaillés sur la description morphologique et l'identification taxonomique afin d'aider à la normalisation de la classification des phlébotomes en Asie du Sud-Est. Nous avons observé une différenciation selon les provinces en termes de densité et de richesse en espèces, avec Lang Son ayant la plus forte densité et Ninh Binh ayant la plus grande richesse en espèces. La majorité des spécimens ont été collectés dans des grottes rocheuses et à l'extérieur, suggérant principalement des caractères cavernicoles et exophiles des espèces de phlébotomes du nord du Vietnam. Cependant, des spécimens ont également été collectés dans des sites intra et péri-domiciliaires. Il convient de noter que Ph. stantoni était la principale espèce trouvée dans les abris pour chiens et à l'intérieur, notamment dans la maison d'un patient atteint de leishmaniose.

Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children.

The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analyzed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titers decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.

Resistance mechanisms and genetic relatedness among carbapenem-resistant Pseudomonas aeruginosa isolates from three major hospitals in Hanoi, Vietnam (2011-15).

BACKGROUND: MDR bacteria including carbapenem-resistant Pseudomonas aeruginosa are recognized as an important cause of hospital-acquired infections worldwide. This investigation seeks to determine the molecular characterization and antibiotic resistance genes associated with carbapenem-resistant P. aeruginosa. METHODS: We conducted WGS and phylogenetic analysis of 72 carbapenem-resistant P. aeruginosa isolated from hospital-acquired infection patients from August 2011 to March 2015 in three major hospitals in Hanoi, Vietnam. RESULTS: We identified three variants of IMP gene, among which bla IMP-15 was the most frequent (n = 34) in comparison to bla IMP-26 (n = 2) and bla IMP-51 (n = 12). We observed two isolates with imipenem MIC >128 mg/L that co-harboured bla IMP-15 and bla DIM-1 genes and seven isolates (imipenem MIC > 128 mg/L) with a bla KPC-1 gene from the same hospital. MLST data shows that these 72 isolates belong to 18 STs and phylogenetic tree analysis has divided these isolates into nine groups. CONCLUSIONS: Our results provide evidence that not only bla IMP-26 but other IMP variants such as bla IMP-15 and bla IMP-51 genes and several STs (ST235, ST244, ST277, ST310, ST773 and ST3151) have been disseminating in healthcare settings in Vietnam. In addition, we report the emergence of two isolates belonging to ST1240 and ST3340 that harboured two important carbapenemase genes (bla IMP-15 and bla DIM-1) and seven isolates belonging to ST3151 of P. aeruginosa that carried the bla KPC-1 gene in Vietnam, which could potentially cause serious restricted availability of treatment options in healthcare settings.

BCL-XL antagonism selectively reduces neutrophil life span within inflamed tissues without causing neutropenia.

Neutrophils help to clear pathogens and cellular debris, but can also cause collateral damage within inflamed tissues. Prolonged neutrophil residency within an inflammatory niche can exacerbate tissue pathology. Using both genetic and pharmacological approaches, we show that BCL-XL is required for the persistence of neutrophils within inflammatory sites in mice. We demonstrate that a selective BCL-XL inhibitor (A-1331852) has therapeutic potential by causing apoptosis in inflammatory human neutrophils ex vivo. Moreover, in murine models of acute and chronic inflammatory disease, it reduced inflammatory neutrophil numbers and ameliorated tissue pathology. In contrast, there was minimal effect on circulating neutrophils. Thus, we show a differential survival requirement in activated neutrophils for BCL-XL and reveal a new therapeutic approach to neutrophil-mediated diseases.

Successful containment of a flight-imported COVID-19 outbreak through extensive contact tracing, systematic testing and mandatory quarantine: Lessons from Vietnam.

BACKGROUND: The importation of SARS-CoV-2 through air travel poses substantial risks to generate new COVID-19 outbreaks. Timely contact tracing is particularly crucial to limit onwards transmission in settings without established community transmission. METHODS: We conducted an in-depth analysis of the response to a big flight-associated COVID-19 outbreak in Vietnam in March 2020 that involved contact tracing, systematic testing and strict quarantine up to third generation contacts. RESULTS: 183 primary contacts from the flight as well as 1000 secondary and 311 third generation contacts were traced, tested, and quarantined across 15 provinces across Vietnam. The protracted confirmation of the index case at 3 days and 19 h after arrival resulted in isolation/quarantine delays of 6.8 days (IQR 6.3-6.8) and 5.8 days (IQR 5.8-7.0) for primary and secondary cases, respectively, which generated 84.0 and 26.4 person-days of community exposure from primary and secondary cases, respectively. Nevertheless, only 5 secondary cases occurred. CONCLUSIONS: A large flight-related COVID-19 cluster was successfully contained through timely, systematic and comprehensive public health responses despite delayed index case identification. Multiagency collaboration and pre-established mechanisms are crucial for low and middle income countries like Vietnam to limit community transmission after COVID-19 importation through air travel.

The Pandemic Experience in Southeast Asia: Interface Between SARS-CoV-2, Malaria, and Dengue.

Southeast Asia (SEA) emerged relatively unscathed from the first year of the global SARS-CoV-2 pandemic, but as of July 2021 the region is experiencing a surge in case numbers primarily driven by Alpha (B.1.1.7) and subsequently the more transmissible Delta (B.1.617.2) variants. While initial disease burden was mitigated by swift government responses, favorable cultural and societal factors, the more recent rise in cases suggests an under-appreciation of prior prevalence and over-appreciation of possible cross-protective immunity from exposure to endemic viruses, and highlights the effects of vaccine rollout at varying tempos and of variable efficacy. This burgeoning crisis is further complicated by co-existence of malaria and dengue in the region, with implications of serological cross-reactivity on interpretation of SARS-CoV-2 assays and competing resource demands impacting efforts to contain both endemic and pandemic disease.

BCL-XL exerts a protective role against anemia caused by radiation-induced kidney damage.

Studies of gene-targeted mice identified the roles of the different pro-survival BCL-2 proteins during embryogenesis. However, little is known about the role(s) of these proteins in adults in response to cytotoxic stresses, such as treatment with anti-cancer agents. We investigated the role of BCL-XL in adult mice using a strategy where prior bone marrow transplantation allowed for loss of BCL-XL exclusively in non-hematopoietic tissues to prevent anemia caused by BCL-XL deficiency in erythroid cells. Unexpectedly, the combination of total body γ-irradiation (TBI) and genetic loss of Bcl-x caused secondary anemia resulting from chronic renal failure due to apoptosis of renal tubular epithelium with secondary obstructive nephropathy. These findings identify a critical protective role of BCL-XL in the adult kidney and inform on the use of BCL-XL inhibitors in combination with DNA damage-inducing drugs for cancer therapy. Encouragingly, the combination of DNA damage-inducing anti-cancer therapy plus a BCL-XL inhibitor could be tolerated in mice, at least when applied sequentially.

Defining the susceptibility of colorectal cancers to BH3-mimetic compounds.

Novel targets are required to improve the outcomes for patients with colorectal cancers. In this regard, the selective inhibitor of the pro-survival protein BCL2, venetoclax, has proven highly effective in several hematological malignancies. In addition to BCL2, potent and highly selective small molecule inhibitors of its relatives, BCLxL and MCL1, are now available, prompting us to investigate the susceptibility of colorectal cancers to the inhibition of one or more of these pro-survival proteins. While targeting BCLxL, but not BCL2 or MCL1, on its own had some impact, most (15/17) of the immortalized colorectal cancer cell lines studied were efficiently killed by the combined targeting of BCLxL and MCL1. Importantly, these in vitro findings were confirmed in a xenograft model and, interestingly, in all (5/5) patient derived tumor organoids evaluated. Our results lend strong support to the notion that BCLxL and MCL1 are highly promising targets for further evaluation in efforts to improve the treatment of colorectal cancers.

Epidemiological and comparative genomic analysis of Bacillus anthracis isolated from northern Vietnam.

To understand the epidemiological and genetic background of anthrax cases occurring in Vietnam from 2011 to 2015, we surveilled and genetically analyzed Bacillus anthracis isolated in the north of the country. Epidemiological surveillance showed that most human cutaneous anthrax cases occurred in association with animal dissection. Whole-genome sequences were obtained from six B. anthracis strains from human patients with cutaneous anthrax in the endemic area. Comparative genomic analysis showed that the genetic homogeneity among Vietnamese B. anthracis strains was very high. All Vietnamese B. anthracis strains belonged to the canSNP lineage of A.Br.011/009, which mostly consists of strains of the trans-Eurasian (TEA) group, including the most closely related strain, Carbosap. To clarify the genetic diversity of Vietnamese strains and strains belonging to A.Br.011/009 and A.Br.008/011 canSNP lineages, we applied a reference genome-based single-nucleotide polymorphism (SNP) and gene-by-gene genomic analysis (whole-genome MLST) strategy. The phylogeny from core genome SNPs revealed that the Vietnamese strains were positioned close to each other; moreover, several SNPs specific to Vietnamese B. anthracis were identified. Whole-genome MLST analysis revealed the differences in the number of SNPs between Vietnamese strains, which could enable discrimination at the strain level.

Sero-Prevalence Surveillance to Predict Vaccine-Preventable Disease Outbreaks; A Lesson from the 2014 Measles Epidemic in Northern Vietnam.

BACKGROUND: During the first half of 2014, a severe outbreak of measles occurred in northern Vietnam, causing 15 033 confirmed cases and 146 deaths. METHODS: To evaluate the population-level seroprevalence of protection against measles in the period before the outbreak, we made use of an existing age-stratified serum bank, collected over the year before the outbreak, between November 2012 and December 2013, from 4 sites across the country (Hanoi, Hue, Dak Lak, and Ho Chi Minh City). Data from the UNICEF's Multiple Indicator Clustered Surveys (MICS), carried out in Vietnam during the first quarter of 2014, were used to assess the vaccine coverage in 6 ecological regions of Vietnam. RESULTS: Results revealed a large discrepancy between levels of protection, as estimated from the serology and vaccine coverage estimated by UNICEF's MICS. Variation in seroprevalence across locations and age groups corresponded with reported numbers of measles cases, most of which were among the 0-2-year-old age group and in the northern part of the country. CONCLUSIONS: Our study presents a strong case in favor of a serosurveillance sentinel network that could be used to proactively tune vaccination policies and other public health interventions.

Incidence of dengue and chikungunya viruses in mosquitoes and human patients in border provinces of Vietnam.

BACKGROUND: Dengue virus remains a major threat in Vietnam, while chikungunya virus is expected to become one. Surveillance was conducted from 2012 to 2014 in Vietnam to assess the presence of dengue and chikungunya viruses in patients hospitalized with acute fever in five Vietnam provinces neighboring Lao PDR and Cambodia. Surveillance was extended to mosquitoes present in the vicinity of the patients' households. RESULTS: A total 558 human serum samples were collected along with 1104 adult mosquitoes and 12,041 larvae from 2250 households. Dengue virus was found in 17 (3%) human serum samples and in 9 (0.8%) adult mosquitoes. Chikungunya virus was detected in 2 adult mosquitoes (0.18%) while no chikungunya virus was detected in humans. Differing densities of mosquito populations were found, with the highest in the Long An Province border with Cambodia. Long An Province also displayed the lowest rate of infection, despite a very high Breteau Index, high human population density and presence of the main cross border road system. The highest incidence was found in Dac Nong Province, where the Breteau and Container indices were the second lowest. Dengue virus was detected in five Aedes albopictus, three Aedes aegypti and one Culex vishnui. Chikungunya virus was detected in two Ae. aegypti. All infected mosquitoes belonged to haplotypes described in other parts of the world and a number of novel haplotypes were found among uninfected mosquitoes. CONCLUSIONS: Dengue is considered to be regularly introduced to Vietnam from Cambodia, mostly through human movement. The data reported here provides a complementary picture. Due to intensive international trade, long-distance transportation of mosquito populations may play a role in the regular importation of dengue in Vietnam through Ho Chi Minh City. It is important to decipher the movement of mosquitoes in Vietnam, not only at the Lao PDR and Cambodia borders but also through international trade routes. Mosquito surveillance programs should address and follow mosquito populations instead of mosquito species.

Synthesis of Chromones from 1,1-Diacylcyclopropanes: Toward the Synthesis of Bromophycoic Acid E.

A tandem deprotection-cyclization reaction of 1,1-diacylcyclopropanes is described which allows rapid access to structurally diverse 2,3-disubstituted chromones in good yields, and with straightforward purification. The utility of this reaction is showcased by the construction of the potent antibacterial marine natural product bromophycoic acid E scaffold.